MCW new NLP Service

All, We have a new NLP Service publically available : https://cis.ctsi.mcw.edu/nlp/ Documentation to follow. G George Kowalski BS Biomedical Engineer Biomedical Informatics (414) 805-7318 (office) gkowal...@mcw.edu ___

Re: Running the PCORNet EDC SAS on Linux

Ours ran , no issues . Would a copy of the log be useful ? I can send it to you via your securefiles.ku.edu web site. G From: Gpc-dev on behalf of Michael Prittie Date: Wednesday, June 21, 2017 at 9:03 AM To: "gpc-dev@listserv.kumc.edu"

Re: help moving CDM SAS to linux

Dan, We run sas on linux and have not seen it on any queries, but we’re not running the new CDM Beta code . If we can get the new i2p_transform code to connect to Oracle , We’re chomping at the bit to try this out . G From: Gpc-dev on behalf of Dan

combining notes

All , Per yesterday’s call: Not much to the code to combine text notes . Our main query is : SELECT pm.date_off, hnt.* FROM hno_note_text hnt LEFT OUTER JOIN patient_mapping pm ON hnt.pat_id = pm.pat_id WHERE hnt.note_id IS NOT NULL AND hnt.pat_id IS NOT NULL ORDER BY

Re: Linking Geocoding data with i2b2

Phil, I just created the table in oracle , shooting from the hip : CREATE TABLE MCW_GEOCODING ( OID INTEGER, JOIN_COUNT INTEGER, TARGET_FID INTEGER, LOC_NAME VARCHAR2(200), STATUS VARCHAR2(200), SCORE INTEGER, MATCH_TYPE

question on GROUSE Extract

All, Per todays call referencing ticket (https://informatics.gpcnetwork.org/trac/Project/ticket/595 ), we've had further discussion here at MCW and have a question. Is this extract only for Grouse at this time or is this going to be also be used for the "Cancer CRG" with this initial pull?

the Encounter Types for Insurance Coverage

All, Per todays GPC Call : Here ( at MCW ) are the Encounter Types we determined were to be included when looking for Insurance Coverage ENC_TYPE_C NAME 99 Billing Encounter 1000 Cardiology Consult Visit 500526 Cardiology Nurse Only Visit 500522 Cardiology Office Visit 223 Cardiology

FW: Med Coll Wisconsin's r003 approved

We’ve been approved. From: "Kowalski, George" <gkowal...@mcw.edu> Date: Monday, April 24, 2017 at 8:44 AM To: CRDW <c...@mcw.edu> Subject: FW: Med Coll Wisconsin's r003 approved From: PCORnet DRN OC <dr...@pcornet.org> Date: Monday, April 24, 2017 at 8:43 AM T

Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

“Database Error” when I expand them. G From: Gpc-dev <gpc-dev-boun...@listserv.kumc.edu> on behalf of "Kowalski, George" <gkowal...@mcw.edu> Date: Wednesday, April 12, 2017 at 8:04 AM To: "gpc-dev@listserv.kumc.edu" <gpc-dev@listserv.kumc.edu> Subject: Re: [gpc-

Re: [gpc-informatics] #280: Medication ontology orgainzed by ingredient

I’ve emptied our terms table until such time as we can determine what’s going wrong with the import process. From: Gpc-dev <gpc-dev-boun...@listserv.kumc.edu> on behalf of "Kowalski, George" <gkowal...@mcw.edu> Date: Wednesday, April 12, 2017 at 8:00 AM To: "gpc-dev@

Re: about the Babel problem

So what’s file file size limit now ? From: Gpc-dev on behalf of Debbie Yoshihara Date: Monday, April 10, 2017 at 9:38 AM To: Nathan Graham , Lav Patel Cc: gpc-dev Subject: Re:

Re: [Gpc-deid] Agenda for todays webex meeting

VERHAGEN <verhagen.lau...@mcrf.mfldclin.edu> Date: Friday, April 7, 2017 at 11:20 AM To: "Kowalski, George" <gkowal...@mcw.edu> Subject: RE: [Gpc-deid] Agenda for todays webex meeting Hi George, What meeting? When? Thanks, Laurel -Original Message- From: Gpc-deid

Re: MCW Shrine demographics online

Yes , per your email , that’s the SHRINE Ontology I’ve loaded and the one I’m mapping to . http://imgur.com/a/h1qza G From: Phillip Reeder <phillip.ree...@utsouthwestern.edu> Date: Monday, April 3, 2017 at 5:08 PM To: "Kowalski, George" <gkowal...@mcw.edu> Cc: &quo

MCW Shrine demographics online

All, I’ve mapped the SHRINE demographics concepts from our ontology to the SCHILS ontology in case anyone wants to test against our server. It’s pointing to our production I2B2 instance so you will get back real numbers. I still get errors from all the other sites for any of the demographic

MCW Shrine is online

All, MCW’s shrine is online, upgraded, and talking to the UWM hub after all the help Keith provided us this week. ( Ale Asylum – Hopalicious for you ) We now have the task of mapping thru the Concept codes to our Ontologies. George ___ Gpc-dev

GPC-DEID discussion list started

FYI , There is a new Text Notes De-identification discussion list we’ve started : http://listserv.kumc.edu/mailman/listinfo/gpc-deid The purpose of this group is to discuss the technical aspects of the De-identification Software that the GPC is using. Feel free to join if you wish to listen

Re: re-subscribe me please

Thanks , got it ! From: Hillary Sandoval <hsando...@kumc.edu> Date: Tuesday, February 14, 2017 at 10:18 AM To: "Kowalski, George" <gkowal...@mcw.edu> Cc: "'Gpc-dev@listserv.kumc.edu'" <Gpc-dev@listserv.kumc.edu> Subject: RE: re-subscribe me please Hi Georg

re-subscribe me please

Can some one please send me the meeting invite ( the outlook one with the link to the meeting ) for the GPC-DEV call ? It fell off my calendar somehow. Thanks G George Kowalski BS Biomedical Engineer Biomedical Informatics (414) 805-7318 (office) gkowal...@mcw.edu

Deid and docker presentation

Here is my presentation from the GPC-DEV Hackathon : https://docs.google.com/presentation/d/1PyPSTb9IJnOasKtME2RaZAfJOQ3ju8ODbMSqD5B84NI/edit?usp=sharing ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu

Re: PCORnet Front Door #3 Parkinson's queries

Thanks , I poked around in the Datamart client tool but only looked at the first datamart , which does not have this setting , the other one does. G George Kowalski - (414) 805-7318 From: Michael Prittie <mprit...@kumc.edu> Date: Tuesday, January 3, 2017 at 10:48 AM To: "Kowal

PCORnet Front Door #3 Parkinson's queries

All, FYI : the 5 queries that have come thru for this study are all hard coded to the “cdm” schema , if your using another schema name in your cdm v3 you’ll have issues running them . We’re working with PCORNet to get this addressed. G George Kowalski - (414) 805-7318

Re: UNMC -- BC survey -- issue with rxcui values for importing per-medication into RedCap, rxcui values

Use Russ’s , We’re seeing him stand up there talking right now. Is there a live feed ? G George Kowalski Biomedical Informatics Software Engineer Clinical & Translational Science Institute Medical College of Wisconsin 9200 West Wisconsin Avenue, Suite L722A Milwaukee, Wisconsin USA 53226

Re: [gpc-informatics] #328: Codebook for breast cancer aggregated-response dataset

:gkowal...@mcw.edu> From: GPC Informatics <d...@madmode.com> Reply-To: "gpc-dev@listserv.kumc.edu" <gpc-dev@listserv.kumc.edu> Date: Monday, September 26, 2016 at 4:15 PM To: "dconno...@kumc.edu" <dconno...@kumc.edu>, "Kowalski, George" <gk

ALS Survey with EMR data - DE-IDENTIFIED Completed for MCW

MCW has uploaded it’s records into the “ALS Survey with EMR data - DE-IDENTIFIED” redcap survey . G George Kowalski Biomedical Informatics Software Engineer Clinical & Translational Science Institute Medical College of Wisconsin 9200 West Wisconsin Avenue, Suite L722A Milwaukee, Wisconsin USA

Re: Data Fulfillment form: please review RE: GPC Dev agenda

Ahh , I was confused by the “Everybody please take a look” ☺ George Kowalski Biomedical Informatics Software Engineer Clinical & Translational Science Institute Medical College of Wisconsin 9200 West Wisconsin Avenue, Suite L722A Milwaukee, Wisconsin USA 53226 414.805.7318 (office) /

Locked out of DataMart Client

Anyone know whom to contact support to unlock my account for the datamart client ? I tried supp...@popmednet.org They referred me to h...@pcornet.org . No answer from them and we have results to return . Thanks G George Kowalski Biomedical Informatics Software

PCORnet Modular Program 1 Request Completed

From today’s call : LV - MCW should have received PMP-1 at the same time as KUMC. Alexander to ask George We ran the query and submitted the requested data back to PCORI last week. G George Kowalski Biomedical Informatics Software Engineer Clinical & Translational Science Institute Medical

Re: gpc-dev 10 May meeting?

Yes I am . G George Kowalski 414.805.7318 (office) / gkowal...@mcw.edu From: > on behalf of Dan Connolly > Date: Tuesday, May 10, 2016 at 9:42

PROD_P02_DQA_FDPRO_DIAQ_NSD6_r001 SAS query

All, The SAS script references a HARVEST table . In this table what are the NETWORKID , NETWORK_NAME, DATAMARTID and DATAMART_NAME we should be using ? Thanks G George Kowalski Biomedical Informatics Software Engineer Clinical & Translational Science Institute Medical College of

Re: data issues

Bradley, W When you say there are “ Duplicate records (indicated with equivalent sequence number”, what field are you basing this off of ? http://www.naaccr.org/Applications/ContentReader/default.aspx?c=9 shows only two sequence numbers , both with not enough room to make each tumor unique

gpc-qa-quarterly repo updated 1/201/6

All , REPO has been updated with the latest Oracle code from Phillip : https://bitbucket.org/gpcnetwork/gpc-qa-quarterly/ G George Kowalski Biomedical Informatics Software Engineer Clinical & Translational Science Institute Medical College of Wisconsin 9200 West Wisconsin Avenue, Suite L722A

Re: Oracle QA Queries

All, Try as I might, no permissions to push this code to the https://bitbucket.org/gpcnetwork/gpc-qa-quarterly repo for me. We’ll have to wait for Dan. G George Kowalski 414.805.7318 (office) / gkowal...@mcw.edu From:

Clarification on permissions within the PCORNet queries

All, Just an FYI on the Query tool I wanted clarification on. From: Sturtevant, Jessica Date: Friday, February 13, 2015 at 8:53 AM To: Kowalski, George Cc: LAUREL VERHAGEN, Jenny Ibarra (jenny.iba...@duke.edu) Subject: RE: MCW Ready with ver 5 client Hi George, This is a very good

Re: PopMedNet node at UNMC

Laurel, I have the 5.0 DataMart client connected to the: https://api.pcornet.org Service URL and it seems to be working like the first time . Assuming we don’t have to hook it up to the “fake Postgres” data, we’re ready to go here at MCW for the Basic Query. Thanks George From: Justin

Re: agenda gpc-dev 8 Apr 11amCT

All, Online Meeting notes for the 11:00am meeting can be found here : http://bit.ly/1eopWKE George Kowalski Biomedical Informatics Software Engineer Clinical Translational Science Institute Medical College of Wisconsin 9200 West Wisconsin Avenue, Suite L722A Milwaukee, Wisconsin USA 53226